{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:07:58Z","timestamp":1789477678927,"version":"build-2803163510"},"reference-count":42,"publisher":"American Chemical Society (ACS)","issue":"26","license":[{"start":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T00:00:00Z","timestamp":1575849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_ccbyncnd_termsofuse.html"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Building on previous work (J. Phys. Chem. A\u00a02017,\u00a0121, 8154\u20138166) under neutral conditions, we examined the co-oligomerization of CH2O and pyrrole to form porphryinogen under acidic conditions using density functional theory (B3LYP\/\/6-311G**). Thermodynamically, we found that azafulvene intermediates were significantly stabilized under highly acidic conditions. Kinetically, energy barriers were lowered for C\u2013C bond formation, discriminating in favor of reactions that lead to porphyrinogen. However, it was challenging to satisfactorily combine our thermodynamic and kinetic profiles into a unified free-energy profile because of difficulties in optimizing transition states of cationic species involving proton hops. Instead, we used neutral carboxylic acids as a proxy to study how energy barriers changed. By combining data from both neutral and acidic conditions, we estimate a free-energy profile for the initial steps of oligomerization under milder acidic conditions more relevant to prebiotic chemistry.<\/jats:p>","DOI":"10.1021\/acsomega.9b03931","type":"journal-article","created":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T14:15:20Z","timestamp":1575900920000},"page":"22251-22259","source":"Crossref","is-referenced-by-count":5,"title":["Role of Acid in\nthe Co-oligomerization of Formaldehyde\nand Pyrrole"],"prefix":"10.1021","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-1887","authenticated-orcid":true,"given":"Jeremy","family":"Kua","sequence":"first","affiliation":[{"name":"University of San Diego , , 5998 Alcala Park , , ,","place":["San Diego, California, United States, 92110"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alyssa S.","family":"Miller","sequence":"additional","affiliation":[{"name":"University of San Diego , , 5998 Alcala Park , , ,","place":["San Diego, California, United States, 92110"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camryn E.","family":"Wallace","sequence":"additional","affiliation":[{"name":"University of San Diego , , 5998 Alcala Park , , ,","place":["San Diego, California, United States, 92110"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Loli","sequence":"additional","affiliation":[{"name":"University of San Diego , , 5998 Alcala Park , , ,","place":["San Diego, California, United States, 92110"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2019,12,9]]},"reference":[{"key":"2026091508274960400_cit1","doi-asserted-by":"publisher","first-page":"8154","DOI":"10.1021\/acs.jpca.7b08685","article-title":"Porphinogen Formation from the Co-Oligomerization of Formaldehyde\nand Pyrrole: Free Energy Pathways","volume":"121","author":"Kua","year":"2017","journal-title":"J. Phys.\nChem. A"},{"key":"2026091508274960400_cit2","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1071\/ch9641028","article-title":"Porphyrins.\nVII. The synthesis of\nporphyrins by the Rothemund reaction","volume":"17","author":"Badger","year":"1964","journal-title":"Aust.\nJ. Chem."},{"key":"2026091508274960400_cit3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1038\/216029a0","article-title":"Porphyrin Abiogenesis\nfrom Pyrrole and Formaldehyde\nunder Simulated Geochemical Conditions","volume":"216","author":"Hodgson","year":"1967","journal-title":"Nature"},{"key":"2026091508274960400_cit4","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1089\/ast.2012.0934","article-title":"A Possible Prebiotic Origin on Volcanic Islands of\nOligopyrrole-Type Photopigments and Electron Transfer Cofactors","volume":"13","author":"Fox","year":"2013","journal-title":"Astrobiology"},{"key":"2026091508274960400_cit5","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1002\/jhet.5570070205","article-title":"Porphyrinogens\nand porphodimethenes, intermediates in the synthesis ofmeso-tetraphenylporphins\nfrom pyrroles and benzaldehyde","volume":"7","author":"Dolphin","year":"1970","journal-title":"J. Heterocycl.\nChem."},{"key":"2026091508274960400_cit6","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1021\/jo00381a022","article-title":"Rothemund\nand Adler-Longo reactions revisited: synthesis of tetraphenylporphyrins\nunder equilibrium conditions","volume":"52","author":"Lindsey","year":"1987","journal-title":"J. Org. Chem."},{"key":"2026091508274960400_cit7","doi-asserted-by":"publisher","first-page":"10025","DOI":"10.1039\/c5ob01409c","article-title":"Paley\u2019s Watchmaker Analogy and Prebiotic Synthetic\nChemistry in Surfactant Assemblies. Formaldehyde Scavenging by Pyrroles\nLeading to Porphyrins as a Case Study","volume":"13","author":"Alexy","year":"2015","journal-title":"Org.\nBiomol. Chem."},{"key":"2026091508274960400_cit8","doi-asserted-by":"publisher","first-page":"2010","DOI":"10.1021\/ja01313a510","article-title":"Formation\nof Porphyrins from Pyrrole and Aldehydes","volume":"57","author":"Rothemund","year":"1935","journal-title":"J.\nAm. Chem. 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Soc."},{"key":"2026091508274960400_cit33","doi-asserted-by":"publisher","first-page":"2335","DOI":"10.1021\/ja409036c","article-title":"Mechanism\nof O2 Activation and Methanol Production by (Di(2-pyridyl)methanesulfonate)PtIIMe(OHn)(2-n)-\nComplex from Theory with Validation from Experiment","volume":"136","author":"Liu","year":"2014","journal-title":"J. Am. Chem. Soc."},{"key":"2026091508274960400_cit34","doi-asserted-by":"publisher","first-page":"12658","DOI":"10.1021\/jp4098292","article-title":"Mapping the Kinetic\nand Thermodynamic Landscape of Formaldehyde Oligomerization under\nNeutral Conditions","volume":"117","author":"Kua","year":"2013","journal-title":"J. Phys. Chem. 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